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Net charge on peptide

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Consider this peptide:


What is the net charge of this peptide at ph=1
What is the net charge of this peptide at ph=7

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To determine net charge on a peptide, you have to look at the pKa value for the different ionizing groups. That's the key.

In considering the structure of this peptide, we need to know what Phe-Glu-Ser-Met means. Peptides are always written with the N-terminal amino acid on the left side. Therefore, the structure is actually N-Phe-Glu-Ser-Met-C.

Knowing this, we can now list all of the ionizable groups in this tetrapeptide. I will use the pKa values on p. 113 of the second edition of Principles of Biochemistry (Lehninger, Nelson, Cox). If the values in your textbook are slightly different than these, that's okay. It shouldn't change the results too much.

There is no ionizable group in the R group in phenylalanine. Therefore, the only ionizable group we need to consider is the N-terminal group. Its pKa is 9.13. (Of course, the COOH group in phenylalanine doesn't exist in the peptide because it's involved in a peptide bond with glutamate.)

Both NH2 and COOH groups in glutamate don't exist because of the peptide bonds with phenylalanine ...

Solution Summary

The expert examines net charge on peptide for Phe-Glu-Ser-Met.

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Amino Acid Problems

(See attached file for full problem description)

9. An organism of unknown origin produces a potent inhibitor of nerve conduction which you wish to sequence. Amino acid analysis shows the peptide's composition to be 5 Ala, 1 Lys, 1 Phe. Reaction of the intact peptide with phenylisothiocyanate (Edman's reagent) followed by treatment with trifluoroacetic acid liberates a phenylthiohydantoin (PTH)-derivative of alanine. Trypsin cleavage of the intact peptide gives a tripeptide and a tetrapeptide, with compositions 3 Ala, 1 Phe and 1 Lys, 2 Ala. Reaction of the intact peptide with chymotrypsin yields a hexapeptide plus free alanine. What is the inhibitor's sequence? (Justify your answer by explaining how each treatment would produce the observed products.)

10. A solution which contains a mixture of three tripeptides -- 1) Tyr-Lys-Thr, 2) Asp-Met-Ala, and 3) Asp-Cys-Arg -- is spotted in the middle of three strips of filter paper. Each strip is then subjected to paper electrophoresis at a different pH: 2.0, 6.0, and 13.0. Sketch the patterns of separation you would expect for these tripeptides at each of these pHs, indicating their positions relative to one another and to the anode (i.e., + electrode), spot of application (i.e., origin), and cathode (i.e., - electrode). See Table 4.1 in the Garrett and Grisham text for pKas. Hint: the separation is based on the net charge carried by the peptides.

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